RNA-based boronate internucleosidic linkages: an entry into reversible templated ligation and loop formation

Area of Science:

• Supramolecular chemistry
• Biochemistry
• Molecular biology

Background:

• Supramolecular biopolymers offer control over assembly and disassembly for engineering new biomaterials.
• Nucleic acid-based systems are promising for creating defined, stimuli-responsive molecular architectures.

Purpose of the Study:

• To synthesize a novel 5'-boronoribonucleotidic phosphoramidite building block.
• To demonstrate its utility in templated ligation for creating boronate internucleosidic linkages.
• To investigate the formation of RNA loops using 5'-boronic acid-ended RNA sequences.

Main Methods:

• Synthesis of a 5'-boronoribonucleotidic phosphoramidite building block.
• RNA- and DNA-templated ligation reactions.
• Melting denaturation studies.
• Molecular-dynamics (MD) simulations.

Main Results:

• Successful synthesis and incorporation of the 5'-boronoribonucleotidic building block into RNA.
• Demonstration of RNA- and DNA-templated ligation to form boronate internucleosidic linkages.
• Evidence of 5'-boronic acid-ended RNA promoting RNA loop formation with RNA templates.
• MD simulations provided insights into structural parameters governing these processes.

Conclusions:

• The developed building block facilitates the creation of novel nucleic acid-based supramolecular structures.
• This approach enables the engineering of stimuli-responsive molecular architectures with potential applications in biomaterials and biological systems modulation.
• The findings open new avenues for designing complex, self-assembled nucleic acid systems.